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- PDB-1w99: Mosquito-larvicidal toxin Cry4Ba from Bacillus thuringiensis ssp.... -

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Basic information

Entry
Database: PDB / ID: 1w99
TitleMosquito-larvicidal toxin Cry4Ba from Bacillus thuringiensis ssp. Israelensis
ComponentsPESTICIDIAL CRYSTAL PROTEIN CRY4BA
KeywordsTOXIN / MEMBRANE PORE / BIO-INSECTICIDE / DIPTERAN SPECIFICITY / CONFORMATIONAL CHANGE / HYDROPHOBIC PATCH
Function / homology
Function and homology information


symbiont-mediated killing of host cell / sporulation resulting in formation of a cellular spore / toxin activity / signaling receptor binding
Similarity search - Function
: / Cry1Ac, domain VII / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / Pesticidal crystal protein, N-terminal domain / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, central domain superfamily / Pesticidal crystal protein, C-terminal ...: / Cry1Ac, domain VII / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / Pesticidal crystal protein, N-terminal domain / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, central domain superfamily / Pesticidal crystal protein, C-terminal / delta endotoxin / Pesticidal crystal protein / Pesticidal crystal protein, N-terminal / Pesticidal crystal protein, N-terminal domain superfamily / delta endotoxin, N-terminal domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Delta-Endotoxin; domain 1 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Pesticidal crystal protein Cry4B protoxin
Similarity search - Component
Biological speciesBACILLUS THURINGIENSIS SEROVAR ISRAELENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.75 Å
AuthorsBoonserm, P. / Li, J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of the Mosquito-Larvicidal Toxin Cry4Ba and its Biological Implications
Authors: Boonserm, P. / Davis, P. / Ellar, D.J. / Li, J.
History
DepositionOct 7, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PESTICIDIAL CRYSTAL PROTEIN CRY4BA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,54127
Polymers63,2611
Non-polymers2,28026
Water10,827601
1
A: PESTICIDIAL CRYSTAL PROTEIN CRY4BA
hetero molecules

A: PESTICIDIAL CRYSTAL PROTEIN CRY4BA
hetero molecules

A: PESTICIDIAL CRYSTAL PROTEIN CRY4BA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,62281
Polymers189,7823
Non-polymers6,84078
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)185.800, 185.800, 187.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1644-

BR

21A-2020-

HOH

31A-2403-

HOH

DetailsTHE TRIMER DESCRIBED HERE IS AN ARTIFACT OF CRYSTALLIZATIONAND DOES NOT REPRESENT THE NATURAL OLIGOMERIC STATE OF THEPROTEIN

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Components

#1: Protein PESTICIDIAL CRYSTAL PROTEIN CRY4BA / DELTA-ENDOTOXIN CRY4BA / INSECTICIDAL DELTA-ENDOTOXIN CRYIVB-A / CRYSTALINE ENTOMOCIDAL PROTOXIN / ...DELTA-ENDOTOXIN CRY4BA / INSECTICIDAL DELTA-ENDOTOXIN CRYIVB-A / CRYSTALINE ENTOMOCIDAL PROTOXIN / MOSQUITO-LARVICIDAL TOXIN CRY4BA


Mass: 63260.762 Da / Num. of mol.: 1 / Fragment: ACTIVATED TOXIN, RESIDUES 84-641
Source method: isolated from a genetically manipulated source
Details: ENTRY CONTAINS ALPHA-HELIX BUNDLE, BETA-PRISM, BETA-SANDWICH DOMAINS. PROTEIN RESIDUES 99,124,219,271,281,361,387,413,348,446,467 AND 476 ARE PRESENT IN TWO ALTERNATE CONFORMATIONS RESIDUES ...Details: ENTRY CONTAINS ALPHA-HELIX BUNDLE, BETA-PRISM, BETA-SANDWICH DOMAINS. PROTEIN RESIDUES 99,124,219,271,281,361,387,413,348,446,467 AND 476 ARE PRESENT IN TWO ALTERNATE CONFORMATIONS RESIDUES 181,346,407,471 AND 452 ARE PRESENT IN THREE ALTERNATE CONFORMATIONS. PROLINE RESIDUES 299,389 AND 414 ARE CIS-PROLINES
Source: (gene. exp.) BACILLUS THURINGIENSIS SEROVAR ISRAELENSIS (bacteria)
Plasmid: CAM135
Production host: BACILLUS THURINGIENSIS SEROVAR ISRAELENSIS (bacteria)
Strain (production host): IPS78/1 E 4 1-3 / References: UniProt: P05519
#2: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRYSTAL STRUCTURE CONTAINS RESIDUES 84-641.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: VAPOUR DIFFUSION AT 20C IN HANGING DROPS CONTAINING 1:1 MIXTURE OF PROTEIN AT 8 MG/ML IN 50 MM SODIUM CARBONATE PH 10.5, 0.1 M SODIUM BROMIDE, 1 MM DTT AND PROTEASE INHIBITORS, AND THE ...Details: VAPOUR DIFFUSION AT 20C IN HANGING DROPS CONTAINING 1:1 MIXTURE OF PROTEIN AT 8 MG/ML IN 50 MM SODIUM CARBONATE PH 10.5, 0.1 M SODIUM BROMIDE, 1 MM DTT AND PROTEASE INHIBITORS, AND THE RESERVOIR BUFFER CONSISTING OF 100MM TRIS ACETATE PH7-8 AND 0.4-0.6 M SODIUM BROMIDE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.75→73.97 Å / Num. obs: 1207111 / % possible obs: 99.6 % / Redundancy: 9.7 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 24.1
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 15.1 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS
Starting model: PDB ENTRY 1DLC, PDB ENTRY 1CIY

1dlc

1ciy


Resolution: 1.75→73.97 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: PRO299, PRO389 AND PRO414 ARE CIS- PROLINES
RfactorNum. reflection% reflectionSelection details
Rfree0.218 6217 5 %RANDOM
Rwork0.205 ---
obs0.205 124587 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.35 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.932 Å2-1.764 Å20 Å2
2---1.932 Å20 Å2
3---3.865 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-73.97 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.75→73.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 33 601 5094
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 1.75→1.81 Å / Rfactor Rfree error: 0.0113 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2773 595 4.8 %
Rwork0.2625 11717 -
obs--99.97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4P6G.PARP6G.TOP

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